I am trying to run BiSeq on RRBS mouse datasets (~60 samples).
I just noticed that my betaResults output only contains chromosomes 1 and 2 (and consequently DMRs output) – does anyone know why this is? Is it because of the betaRegression() function? How could I include all chromosomes?
I have been following the tutorial / introduction (https://www.bioconductor.org/packages/release/bioc/vignettes/BiSeq/inst/doc/BiSeq.pdf) and adapting to my own data. This is however from 2015; does anyone know if there is a more recent tutorial for this?
Any experience / feedback / advice would be truly appreciated.